relating protein abundance & mrna expression mark b gerstein yale (comp. bio. &...
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Relating Protein Abundance & mRNA Expression
Mark B GersteinYale (Comp. Bio. & Bioinformatics)
NIDA site visit at Yale
2007.12.19
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[Greenbaum et al. Bioinformatics 2002, 18, 587.]
Why relate amounts of protein & mRNAGene expression - major place for regulation (easy to measure)
vs. Concentration of protein - major determinant of activity
where ks,i and kd,i are the protein synthesis and degradation rate constants
At steady state: Pi =ks;i [mRNAi ]
kd,i
= ks,i [mRNAi ] – kd,i Pi dPidt
Expectations from simple kinetic models:
Outliers from trend interesting
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[Graphic: Jeong et al, Nature, 41:411]
Protein interaction networks
[Graphic: http://proton.chem.yale.edu]
Protein complexes
In protein complexes, one expects stoichiometric abundance of component proteins and that mRNA expression levels should be correlated with protein abundance
…Among pathways, this is expected to a lesser degree between interacting proteins
Relationship of Protein Abundance to Complexes and Pathways
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mRNA expression levelsMicroarrays
AffymetrixPCR
SAGE
Protein abundance2D Gel Electrophoresis Multiple staining options
Small dynamic range
DIGE Cy3 vs. Cy5 labelingLarge dynamic range
ICAT, iTRAQ MS-basedRelative abundance (ratio of isotopically
labeled species)Large dynamic range
MudPIT LC-MS/MS
SILAC Stable isotope labeling with amino acids in cell culture - for MS analysis
TAP-Tag Weissman and O’Shea (Oct. 2003)
Sources of experimental data
[http://www.biology.ucsc.edu/mcd/images/microarray.gif]
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PARE: proteomics.gersteinlab.org
Upload or use pre-loadedmRNA, protein datasets
Analyze all oranalyze MIPS or GO subset
[Yu et al., BMC Bioinfo. '07]
Open-source codeDownloadable
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PARE: a web-based tool for correlating mRNA expression and protein abundance
PAREmain page
(1) Select mRNA, protein datasets: -use pre-loaded datasets -upload datasets
(2) Choose categorization method: -correlate all -MIPS complexes -GO biological processes -GO molecular function -GO cellular component
Select MIPS, GO subsets (opt.)
Display results (3) Display -Linear or log-log correlation for selected subset(s) -Tabulate data, correlation values for selected subset(s) -Label (on plot) and tabulate outlying datapoints
[Yu et al., BMC Bioinfo. '07]
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Correlated data
Log-log plot of correlation -linear fit -outliers labeled
Calculation of mutual information
PARE output
[Yu
et a
l., B
MC
Bio
info
. '07
]
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Correlation of subsets (GO, MIPS)Yeast ref. datasets: “Correlate all”vs.GO cellular component subsets for particular cellular locations
[Yu
et a
l., B
MC
Bio
info
. '07
]
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PARE: pre-loaded datasets
[Yu et al., BMC Bioinfo. '07]
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Connecting PARE with datasets from NIDA investigators
Protein abundance (iTRAQ datasets)
Mouse (Nairn lab) - samples from 3 brain regions: cortex, striatum, hippocampus
Green monkey (Taylor lab) - several brain regions -caudate, dlPFC, mPFC, NacC, NacS, PFC11, PFC13, PrCO, putameneach treated with saline, PCP, and cocaine
mRNA datasets obtained from expression database
Mouse - Sandberg et al. PNAS 2000, 97, 11038.
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0
0.5
1
1.5
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0 0.5 1 1.5 2 2.5 3mRNA (hippocampus/cortex)
pro
tein
(h
ipp
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mp
us/
cort
ex)
mRNA expression ratio (hippocampus/cortex)
pro
tein
ab
un
dan
ce r
atio
(h
ipp
oca
mp
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Mouse brain: correlation of mRNA & protein expression
For 96 genes with differential expression in hippocampus vs. cortex
Plan to correlate abundance for individual pathways and complexes with C. Bruce ("John", talking later)
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Acknowledgements
iTRAQ datasets:Angus Nairn, Erika Andrade, Dilja KruegerJane TaylorChris Colangelo, Mark Shifman (YPED)
PARE:Anne Burba, Eric Yu